Macromolecular assemblies in DNAassociated functions
• DNA structures: Chromatin (nucleosome)
• Replication complexes: Initiation, progression
Voet Biochemistry 3e
© 2004 John Wiley & Sons, Inc.
• Transcription complexes: Initiation, splicing,
progression
• Other complexes: Repair, recombination
December 23, 2004
TIGP-CBMB Molecular biophysics I
Page 1108
Voet Biochemistry 3e
© 2004 John Wiley & Sons, Inc.
Figure 29-1a Structure of B-DNA. (a) Ball and stick
drawing and corresponding space-filling model viewed
perpendicular to the helix axis.
Page 1124
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© 2004 John Wiley & Sons, Inc.
Figure 29-21
Toroidal and interwound supercoils.
Page 1125
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© 2004 John Wiley & Sons, Inc.
Figure 29-22 Sedimentation rate of underwound closed
circular duplex DNA as a function of ethidium bromide
concentration.
Page 1125
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© 2004 John Wiley & Sons, Inc.
Figure 29-23
X-Ray structure
of a complex of ethidium with 5iodo-UpA.
Figure 31-17 X-Ray structure of actinomycin D
in complex with a duplex DNA of selfcomplementary sequence d(GAAGCTTC).
Voet Biochemistry 3e Page 1127
© 2004 John Wiley & Sons, Inc.
Figure 29-26 X-Ray structure of the Y328F mutant of E.
coli topoisomerase III, a type IA topoisomerase, in complex
with the single-stranded octanucleotide d(CGCAACTT).
Voet Biochemistry 3e Page 1128
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Figure 29-27 Proposed mechanism for the strand
passage reaction catalyzed by type IA topoisomerases.
Page 1129
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Figure 29-28 X-Ray structure of the N-terminally
truncated, Y723F mutant of human topoisomerase I in
complex with a 22-bp duplex DNA.
Voet Biochemistry 3e Page 1131
© 2004 John Wiley & Sons, Inc.
Figure 29-31a Structures of topoisomerase II. (a) X-Ray structure of
the 92-kD segment of the yeast topoisomerase II (residues 410–1202)
dimer.
Page 1131
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© 2004 John Wiley & Sons, Inc.
Figure 29-32 Model for the enzymatic mechanism of type
II topoisomerases.
Voet Biochemistry 3e Page 1423
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Figure 34-1 Electron micrograph of a human metaphase
chromosome and of D. melanogaster chromatin showing that its
10-nm fibers are strings of closely spaced nucleosomes.
Voet Biochemistry 3e Page 1426
© 2004 John Wiley & Sons, Inc.
Figure 34-7a X-Ray structure of the nucleosome core
particle. (a) The entire core particle as viewed (left) along its
superhelical axis and (right) rotated 90° about the vertical axis.
Voet Biochemistry 3e Page 1427
© 2004 John Wiley & Sons, Inc.
Figure 34-3 The amino acid
sequence of calf thymus histone H4.
This 102-residue protein’s 25 Arg
and Lys residues are indicated in
red.
Figure 34-8
X-Ray structure of a histone octamer within the
nucleosome core particle.
Voet Biochemistry 3e Page 1427
© 2004 John Wiley & Sons, Inc.
Figure 34-9
Model of the interaction of histone H1 with
the DNA of the 166-bp chromatosome.
Voet Biochemistry 3e Page 1428
© 2004 John Wiley & Sons, Inc.
Figure 34-10 Electron
micrographs of chromatin.
(a) H1-containing chromatin
and (b) H1-depleted
chromatin, both in 5 to 15
mM salt.
Figure 34-13 Model of the 30-nm
chromatin filament. The filament is
represented (bottom to top) as it
might form with increasing salt
concentration.
Macromolecular assemblies in DNAassociated functions
• DNA structures: Chromatin (nucleosome)
• Replication complexes: Initiation, progression
Voet Biochemistry 3e
© 2004 John Wiley & Sons, Inc.
• Transcription complexes: Initiation, splicing,
progression
• Other complexes: Repair, recombination
December 23, 2004
TIGP-CBMB Molecular biophysics I
Voet Biochemistry 3e Page 1137
© 2004 John Wiley & Sons, Inc.
Figure 30-2
Autoradiogram and its interpretive drawing of a
replicating E. coli chromosome.
Figure 30-1 Action of DNA polymerase. DNA polymerases assemble incoming
deoxynucleoside triphosphates on single-stranded DNA templates such that the
growing strand is elongated in its 5  3 direction.
Voet Biochemistry 3e Page 1155
© 2004 John Wiley & Sons, Inc.
Figure 30-28
The replication of E. coli DNA.
Voet Biochemistry 3e Page 1138
© 2004 John Wiley & Sons, Inc.
Figure 30-5
Semidiscontinuous DNA replication. In DNA
replication, both daughter strands (leading strand red, lagging
strand blue) are synthesized in their 5  3 directions.
Voet Biochemistry 3e Page 1145
© 2004 John Wiley & Sons, Inc.
Table 30-1
Properties of E. coli DNA Polymerases.
Voet Biochemistry 3e Page 1141
© 2004 John Wiley & Sons, Inc.
Figure 30-8a
X-Ray structure of E. coli DNA polymerase I
Klenow fragment (KF) in complex with a dsDNA.
Voet Biochemistry 3e Page 1142
© 2004 John Wiley & Sons, Inc.
Figure 30-9b
X-Ray structure of Klentaq1 in complex with DNA
and ddCTP. (a) The closed conformation. (b) The open
conformation.
Voet Biochemistry 3e Page 1146
© 2004 John Wiley & Sons, Inc.
Figure 30-13a
X-Ray structure of the b subunit of E. coli Pol III
holoenzyme. Ribbon drawing.
Voet Biochemistry 3e Page 1146
© 2004 John Wiley & Sons, Inc.
Table 30-3
Unwinding and Binding Proteins of E. coli
DNA Replication.
Voet Biochemistry 3e Page 1147
© 2004 John Wiley & Sons, Inc.
Figure 30-14 Unwinding of DNA by the combined action
of DnaB and SSB proteins.
Voet Biochemistry 3e Page 1152
© 2004 John Wiley & Sons, Inc.
Table 30-4
Proteins of the Primosomea.
Voet Biochemistry 3e Page 1147
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X-Ray structure of the helicase domain
of T7 gene 4 helicase/primase.
Figure 30-15 Electron microscopy–based image
reconstruction of T7 gene 4 helicase/primase.
Voet Biochemistry 3e Page 1149
© 2004 John Wiley & Sons, Inc.
Figure 30-19 X-Ray structure of the N-terminal 135
residues of E. coli SSB in complex with dC(pC)34.
Voet Biochemistry 3e Page 1151
© 2004 John Wiley & Sons, Inc.
Figure 30-25 Electron micrograph
of a primosome bound to a fX174
RF I DNA. Such complexes
always contain a single
primosome with one or two
associated small DNA loops.
Figure 30-22
X-Ray structure of E. coli primase.
Voet Biochemistry 3e Page 1152
© 2004 John Wiley & Sons, Inc.
Figure 30-23 The synthesis of the
M13 (–) strand DNA on a (+) strand
template to form M13 RF I DNA.
Figure 30-27 The synthesis of
the fX174 (+) strand by the
looped rolling circle mode.
Voet Biochemistry 3e Page 1156
© 2004 John Wiley & Sons, Inc.
Figure 30-29
A model for DNA replication initiation at oriC.
Voet Biochemistry 3e Page 1145
© 2004 John Wiley & Sons, Inc.
Table 30-2
Holoenzyme.
Components of E. coli DNA Polymerase III
Voet Biochemistry 3e Page 1158
© 2004 John Wiley & Sons, Inc.
Figure 30-32
X-Ray structure of the b–d complex.
Voet Biochemistry 3e Page 1159
© 2004 John Wiley & Sons, Inc.
Figure 30-33
complex.
X-Ray structure of the g3dd clamp loading
Voet Biochemistry 3e Page 1159
© 2004 John Wiley & Sons, Inc.
Figure 30-34 Schematic diagram of the clamp loading
cycle. This speculative model is based on a combination of
structural and biochemical information.
Voet Biochemistry 3e Page 1164
© 2004 John Wiley & Sons, Inc.
Figure 30-39 X-Ray structure of RB69 DNA polymerase
(RB69 pol) in complex with primer–template DNA and dTTP.
Macromolecular assemblies in DNAassociated functions
• DNA structures: Chromatin (nucleosome)
• Replication complexes: Initiation, progression
Voet Biochemistry 3e
© 2004 John Wiley & Sons, Inc.
• Transcription complexes: Initiation, splicing,
progression
• Other complexes: Repair, recombination
December 23, 2004
TIGP-CBMB Molecular biophysics I
Voet Biochemistry 3e Page 1449
© 2004 John Wiley & Sons, Inc.
Figure 34-42 Immunofluorescence micrograph of a
lampbrush chromosome from an oocyte nucleus of the newt
Notophthalmus viridescens.
Voet Biochemistry 3e Page 1452
© 2004 John Wiley & Sons, Inc.
Figure 34-47 Assembly of the preinitiation complex (PIC)
on a TATA box–containing promoter.
Voet Biochemistry 3e Page 1453
© 2004 John Wiley & Sons, Inc.
Figure 34-48a
X-Ray structure of Arabidopsis thaliana TATA box–
binding protein (TBP). (a) A ribbon diagram of the protein in the absence of
DNA. (b) TBP with a 14-bp TATA box–containing segment DNA.
Voet Biochemistry 3e Page 1454
© 2004 John Wiley & Sons, Inc.
Figure 34-49 Model of the TFIIA–TFIIB–TBP–TATA box–
containing DNA quaternary complex.
Voet Biochemistry 3e Page 1454
© 2004 John Wiley & Sons, Inc.
Figure 34-50 EM-based image of the human TFIID–
TFIIA–TFIIB complex at 35-Å resolution.
Voet Biochemistry 3e Page 1222
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Figure 31-9
An electron micrograph of E. coli RNA
polymerase (RNAP) holoenzyme attached to various
promoter sites on bacteriophage T7 DNA.
Voet Biochemistry 3e Page 1223
© 2004 John Wiley & Sons, Inc.
Figure 31-10 The sense (nontemplate) strand sequences
of selected E. coli promoters.
Voet Biochemistry 3e Page 1224
© 2004 John Wiley & Sons, Inc.
Figure 31-11a X-Ray structure of Taq RNAP core enzyme. a
subunits are yellow and green, b subunit is cyan, b subunit is
pink, w subunit is gray. (b) The holoenzyme viewed as in Part a.
Voet Biochemistry 3e Page 1234
© 2004 John Wiley & Sons, Inc.
Figure 31-21b X-Ray structure of an RNAP II elongation
complex.
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Figure 31-47
The sequence of steps in the production of mature
eukaryotic mRNA as shown for the chicken ovalbumin gene. The
consensus sequence at the exon–intron junctions of vertebrate premRNAs.
Voet Biochemistry 3e Page 1259
© 2004 John Wiley & Sons, Inc.
Figure 31-49 The sequence of transesterification reactions
that splice together the exons of eukaryotic pre-mRNAs.
Voet Biochemistry 3e Page 1261
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Figure 31-51a
The self-splicing group I intron from Tetrahymena
thermophila. (a) The secondary structure of the entire 413-nt intron.
(b) The X-ray structure of P4-P6 viewed as in Part a.
Voet Biochemistry 3e Page 1265
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Figure 31-56
action.
An electron micrograph of spliceosomes in
Voet Biochemistry 3e Page 1265
© 2004 John Wiley & Sons, Inc.
Figure 31-57 A schematic diagram of six rearrangements
that the spliceosome undergoes in mediating the first
transesterification reaction in pre-mRNA splicing.
Voet Biochemistry 3e Page 1267
© 2004 John Wiley & Sons, Inc.
Figure 31-60
A model of the snRNP core protein.
Voet Biochemistry 3e Page 1268
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Figure 31-61a
The electron
microscopy-based structure of U1-snRNP
at 10 Å resolution. (a) The predicted
secondary structure of U1-snRNA. (b)
The molecular outline of U1-snRNP. (c)
The U1-snRNA colored as in Part a.
Macromolecular assemblies in DNAassociated functions
• DNA structures: Chromatin (nucleosome)
• Replication complexes: Initiation, progression
Voet Biochemistry 3e
© 2004 John Wiley & Sons, Inc.
• Transcription complexes: Initiation, splicing,
progression
• Other complexes: Repair, recombination
December 23, 2004
TIGP-CBMB Molecular biophysics I
Voet Biochemistry 3e Page 1175
© 2004 John Wiley & Sons, Inc.
Figure 30-54b The structure of E. coli Ada protein. (a) The X-ray
structure of Ada’s 178-residue C-terminal segment, which contains its O6alkylguanine–DNA alkyltransferase function.(b) The NMR structure of
Ada’s 92-residue, N-terminal segment, which mediates its methyl
phosphotriester repair function.
Voet Biochemistry 3e Page 1176
© 2004 John Wiley & Sons, Inc.
Figure 30-55 The mechanism of nucleotide excision
repair (NER) of pyrimidine photodimers.
Voet Biochemistry 3e Page 1178
© 2004 John Wiley & Sons, Inc.
Figure 30-57 X-Ray structure of
human uracil–DNA glycosylase
(UDG) in complex with a 10-bp
DNA containing a U·G base pair.
Figure 30-55 The
mechanism of
nucleotide excision
repair (NER) of
pyrimidine
photodimers.
Voet Biochemistry 3e Page 1184
© 2004 John Wiley & Sons, Inc.
Figure 30-64 The Holliday model of homologous
recombination between homologous DNA duplexes.
Voet Biochemistry 3e Page 1186
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Figure 30-67a Electron micrographs of intermediates in
the homologous recombination of two plasmids. (a) A
figure-8 structure. This corresponds to Fig. 30-66d. (b) A
chi structure that results from the treatment of a figure-8
structure with a restriction endonuclease.
Figure 30-66 Homologous
recombination between two
circular DNA duplexes. This
process can result either in two
circles of the original sizes or in
a single composite circle.
Voet Biochemistry 3e Page 1187
© 2004 John Wiley & Sons, Inc.
Figure 30-68 An electron microscopy–based image
(transparent surface) of an E. coli RecA–dsDNA–ATP
filament.
Voet Biochemistry 3e Page 1188
© 2004 John Wiley & Sons, Inc.
Figure 30-71 The RecA-catalyzed assimilation of a singlestranded circle by a dsDNA can occur only if the dsDNA has
a 3 end that can base pair with the circle (red strand).
Voet Biochemistry 3e Page 1189
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Figure 30-72 A hypothetical model for the RecA-mediated
strand exchange reaction.
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© 2004 John Wiley & Sons, Inc.
Figure 30-75a Proposed structure of the T. thermophilus
RuvB hexamer. (a) EM image reconstruction of RuvB
complexed with DNA (not visible).
Voet Biochemistry 3e Page 1191
© 2004 John Wiley & Sons, Inc.
Figure 30-76 Model of the RuvAB–Holliday junction
complex. The model is based on electron micrographs such
as that in the inset.
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Figure 34-117a Cryoelectron microscopy–based images of the
apoptosome at 27-Å resolution. (a) The free apoptosome. (b)
The apoptosome in complex with a noncleavable mutant of
procaspase-9 in oblique top view.